[ensembl-dev] Feature slice issue

Fri Nov 21 09:22:24 GMT 2014

Hi Konrad,

I can't recreate this issue, but my guess would be it's some combination of
incorrect assembly or FASTA file. Without knowing what setup you're using
it's hard for me to say exactly what.

If I run the following skeleton plugin:

package Skeleton;
use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);

sub run {
  my ($self, $tva) = @_;
  print STDERR "Sequence
".$tva->variation_feature->feature_Slice->expand(1, 1)->seq."\n";
  return {};
}

1;

I get the same results using 75, 76 and 77, using either --database or
--cache with a FASTA file:

2014-11-21 09:19:35 - Read existing cache info
2014-11-21 09:19:35 - Auto-detected FASTA file in cache directory
2014-11-21 09:19:35 - Checking/creating FASTA index
2014-11-21 09:19:35 - Loaded plugin: Skeleton
2014-11-21 09:19:35 - Starting...
2014-11-21 09:19:35 - Detected format of input file as vcf
2014-11-21 09:19:35 - Read 1 variants into buffer
2014-11-21 09:19:35 - Reading transcript data from cache and/or database
[==========]  [ 100% ]
2014-11-21 09:19:35 - Retrieved 185 transcripts (0 mem, 185 cached, 0 DB, 0
duplicates)
2014-11-21 09:19:35 - Analyzing chromosome 1
2014-11-21 09:19:35 - Analyzing variants
[==========]  [ 100% ]
2014-11-21 09:19:35 - Calculating consequences
Sequence GCA
Sequence GCA
...etc...

If using a FASTA file, double check the assembly matches that of your
cache, and re-generate the index. There are also known issues with older
version of BioPerl re: the FASTA indexing - make sure that you are using an
up to date (>1.6) version of BioPerl.

Regards

Will McLaren
Ensembl Variation

On 20 November 2014 21:06, Konrad Karczewski <konradk at broadinstitute.org>
wrote:

> Hi dev team,
>
> I've run into a strange issue when comparing output from v75 and v77. I'm
> looking to get 1 base context around a variant, which I've gotten using:
>
> $transcript_variation_allele->variation_feature->feature_Slice->expand(1,
> 1)->seq;
>
> When running this on a synthetic variant:
>
> 1       12141   .       C       A,T,G   .       .
>
> I get the expected result in v75 (note that context 1 bp around the
> variant is GCA as such:
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1%3A12140-12142
> <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:12140-12142>
> )
>
>
> CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||1|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>A|||||||||||GCA,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||2|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>T|||||||||||GCA,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_exon_variant&nc_transcript_variant|273||||||||3|1/3|||||||1||YES|DDX11L1|HGNC||||processed_transcript||||ENST00000456328.2:n.273C>G|||||||||||GCA,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||1||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>A|||||||||||GCA,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||2||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>T|||||||||||GCA,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&nc_transcript_variant|||||||||3||1/5||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000450305.2:n.49-38C>G|||||||||||GCA,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||1|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>A|||||||||||GCA,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||2|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>T|||||||||||GCA,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_exon_variant&nc_transcript_variant|270||||||||3|1/3|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000515242.2:n.270C>G|||||||||||GCA,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||1|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>A|||||||||||GCA,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||2|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>T|||||||||||GCA,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_exon_variant&nc_transcript_variant|268||||||||3|1/4|||||||1|||DDX11L1|HGNC||||transcribed_unprocessed_pseudogene||||ENST00000518655.2:n.268C>G|||||||||||GCA
>
> but same command/code running under VEP v77, I get this:
>
>
> CSQ=A|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||1||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||2||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||ENST00000456328.2:n.273G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000456328|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|273||||||3||1|DDX11L1|HGNC||processed_transcript|YES||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000450305|Transcript|intron_variant&non_coding_transcript_variant|||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene||||||||||1/5||ENST00000450305.2:n.49-38C>G||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||ENST00000515242.2:n.270G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000515242|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|270||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/3|||||||||||||||||||||||CTT,A|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||1||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>A||||||||||||||||||||CTT,T|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||2||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||ENST00000518655.2:n.268G>T||||||||||||||||||||CTT,G|ENSG00000223972|ENST00000518655|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|268||||||3||1|DDX11L1|HGNC||transcribed_unprocessed_pseudogene|||||||||1/4|||||||||||||||||||||||CTT
>
> Any ideas why this might be the case? Happy to send the plugin and command
> line prompts if that would be helpful.
>
> Thanks!
> -Konrad
>
>
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